There are three "fundamental" ways to do email. One is to use POP3 to download messages to your computer (the approach used by Windows Mail). They then live on your computer. If you don't delete them from the Internet-based mail server, you can also download them to another computer and have copies reside there, also. This approach wasn't designed for synching the mail on the two computers after the fact. Someone might know of a program written to fill this hole, but I'm not familiar with one.
The approach designed for this purpose is used in a networked environment. There is a mail exchange server that performs the synching. It sends and receives mail with the outside world and then allows access to the mail from any computer connected to the network. That isn't an approach that will help you.
The easiest way to sync mail on your computers is to not have to sync it at all, the third approach. There are many web-based email applications that will act as a front-end for other email accounts (they import the mail). You do your email activity online and it all resides there. You can access it from any computer. The equivalent of the Windows Mail software is built into the web site. No syncing is required because you don't have different mail on your computers to sync.
You might want to retain a copy of some or all of the email on a computer for backup or archiving of the messages. The email account probably won't give you infinite storage and you may not want to risk critical messages becoming unavailable because of some problem with your email provider. Pick one of the computers for that purpose and use Windows Mail to download and save the messages you want. In Windows Mail, set the email account you want to archive from to not automatically download messages. That way you can control what and when you archive.
That will take a little manipulation to do it cleanly because with this approach, you generally don't want to download messages until you are done with them unless you don't mind having copies of "in-process" mail on your computer (just don't do anything mail-wize with those messages from your computer; you can easily delete the stuff you don't want). Also, messages sent from your web mail application will not normally be downloaded. Downloading messages will happen only from the web mail's inbox and your computer will keep track of what it has downloaded (it will just download "new" mail, it won't keep downloading everything in the inbox over and over). Some tricks for archiving to your computer:
- Move as needed (temporarily if necessary), mail from folders other than the inbox into the inbox for downloading to your computer. For example, if you want to archive a message from your Sent folder, move the message into the inbox.
- For messages you send that you expect to want to archive, bcc yourself at an email account that you automatically download in Windows Mail but that is not one that you aggregate in your web mail application. These will "automatically" go to your mail archive.
The archiving end of this sounds like a pain in the butt. You don't necessarily have to do it at all, but it isn't as bad as it sounds. Your normal email activity will be automatically "synced" without your having to do anything. The archiving can be done only as needed for specific critical messages, or as a batch that you do maybe once a month.